This is an result for the gene singatures as well as assigned cell type for each cluster based on Danaher et al.
knitr::opts_chunk$set(cache=TRUE)
for( i in 1:length(mean_score[1,])){
print(visualize_me(mean_score[,i],cell_list[i],analysis_results$tsne[c("TSNE.1","TSNE.2")],title=names(cell_list)[i]))
#print(plot(mean_score[,i],type = "h",xlab="Single Cell",ylab=colnames(mean_score)[i]))
h <-hist(mean_score[,i],plot = FALSE)
h<- plot(h, freq = TRUE, labels =TRUE, ylim=c(0, 1.2*max(h$counts)),main=c(names(cell_list)[i]," Score per Single Cell"),xlab=paste(sep=" ",names(cell_list)[i],"Expression Level"),ylab="Numbers of cells")
#lay_out(list(h, 1, 1),
# list(vm, 1, 2))
}




























sig_plot <- visualize_clusters(cluster_tsne$cell_type,cluster_tsne[c("TSNE.1","TSNE.2")],title="Danaher cell-type labels",legend_anno= sort(unique(cluster_tsne[,"name_type"])))+scale_color_manual(values = colorRampPalette(c("blue", "red","yellow"))( length(sort(unique(cluster_tsne[,"name_type"])))))+ annotate("text", x = tsne_center[, 1], y = tsne_center[, 2], size = 5,label=c(1:length(tsne_center[,1])))
sig_plot

counter <-1
colnames(score_by_cluster) <- names(cell_list)
apply(score_by_cluster, 1,function(x) {plot(x,ylab="mean expression level per cell",xlab="cell type", main=c("Cluster",counter))
text(x, names(cell_list), cex=0.6, pos=4, col="red")
sum_table <- kable(all_type_expr_table[all_type_expr_table$Cluster == counter,])
print(sum_table)
cat("\n")
counter <<- counter + 1})

| 3 |
1 |
B_cells |
28 |
55 |
1.527778 |
2.360219 |
963 |
2.9075805 |
0.00519210799584631 |
5 |
1.55951876084647 |
| 4 |
1 |
CD45 |
480 |
1681 |
3.502083 |
3.303695 |
963 |
49.8442368 |
0.811007268951194 |
781 |
42.485291572496 |
| 5 |
1 |
CD8_T_cells |
39 |
114 |
2.651163 |
2.869244 |
963 |
4.0498442 |
0.0306334371754933 |
29.5 |
5.54526825320471 |
| 6 |
1 |
Cytotoxic_cells |
303 |
1376 |
3.192575 |
4.026371 |
963 |
31.4641745 |
0.101246105919003 |
97.5 |
14.522740788157 |
| 7 |
1 |
Exhausted_CD8 |
161 |
284 |
1.690476 |
1.945215 |
963 |
16.7185877 |
0.0490654205607477 |
47.25 |
3.96074487943871 |
| 8 |
1 |
Macrophages |
832 |
5571 |
5.435122 |
3.699126 |
963 |
86.3966771 |
0.63447559709242 |
611 |
24.7512625940577 |
| 9 |
1 |
Neutrophils |
311 |
654 |
1.826816 |
2.112563 |
963 |
32.2949117 |
0.061415220293725 |
59.1428571428571 |
3.70328039909021 |
| 10 |
1 |
NK_CD56dim_cells |
21 |
21 |
1.000000 |
0.000000 |
963 |
2.1806854 |
0.00545171339563863 |
5.25 |
1.14564392373896 |
| 11 |
1 |
NK_cells |
6 |
25 |
3.571429 |
3.207135 |
963 |
0.6230530 |
0.00346140533056421 |
3.33333333333333 |
1.49071198499986 |
| 12 |
1 |
T_cells |
143 |
638 |
2.913242 |
2.991848 |
963 |
14.8494289 |
0.0541709934233299 |
52.1666666666667 |
5.40318835914911 |
| 13 |
1 |
Th1_cells |
9 |
15 |
1.666667 |
2.000000 |
963 |
0.9345794 |
0.0103842159916926 |
10 |
3.46410161513775 |
| 14 |
1 |
Treg |
2 |
2 |
1.000000 |
0.000000 |
963 |
0.2076843 |
0.00207684319833853 |
2 |
1.4142135623731 |

| 15 |
2 |
B_cells |
340 |
795 |
2.048969 |
2.444246 |
11716 |
2.9020143 |
0.00479875573764273 |
56.2222222222222 |
4.36597393430856 |
| 16 |
2 |
CD45 |
3646 |
9692 |
2.658256 |
2.807309 |
11716 |
31.1198361 |
0.420109252304541 |
4922 |
91.323600454647 |
| 17 |
2 |
CD8_T_cells |
2649 |
11130 |
3.312500 |
3.172329 |
11716 |
22.6101058 |
0.221705360191192 |
2597.5 |
60.2349566281906 |
| 18 |
2 |
Cytotoxic_cells |
7866 |
112444 |
5.236042 |
4.343983 |
11716 |
67.1389553 |
0.528857972004097 |
6196.1 |
104.860049589918 |
| 19 |
2 |
DC |
42 |
60 |
1.428571 |
1.563967 |
11716 |
0.3584841 |
0.00128030044383749 |
15 |
2.38047614284762 |
| 20 |
2 |
Exhausted_CD8 |
1778 |
3240 |
1.724321 |
1.991355 |
11716 |
15.1758279 |
0.0455573574598839 |
533.75 |
13.7090298708552 |
| 21 |
2 |
Macrophages |
282 |
408 |
1.441696 |
1.613098 |
11716 |
2.4069648 |
0.00657220894503243 |
77 |
4.83476990145343 |
| 22 |
2 |
Mast_cells |
3 |
10 |
3.333333 |
4.041452 |
11716 |
0.0256060 |
0.000106691703653124 |
1.25 |
0.82915619758885 |
| 23 |
2 |
Neutrophils |
19 |
25 |
1.315789 |
1.376494 |
11716 |
0.1621714 |
0.00024386675120714 |
2.85714285714286 |
0.67005939426049 |
| 24 |
2 |
NK_CD56dim_cells |
173 |
268 |
1.540230 |
1.778514 |
11716 |
1.4766132 |
0.00411829976101058 |
48.25 |
3.92905841137543 |
| 25 |
2 |
NK_cells |
402 |
1033 |
2.275330 |
2.524312 |
11716 |
3.4312052 |
0.0161602367133265 |
189.333333333333 |
10.9341463112378 |
| 26 |
2 |
T_cells |
11147 |
103645 |
4.072815 |
3.460277 |
11716 |
95.1433936 |
0.657647661317856 |
7705 |
85.622556737242 |
| 27 |
2 |
Th1_cells |
305 |
408 |
1.337705 |
1.393378 |
11716 |
2.6032776 |
0.0275691362239672 |
323 |
19 |
| 28 |
2 |
Treg |
84 |
163 |
1.940476 |
2.213601 |
11716 |
0.7169682 |
0.00836462956640492 |
98 |
11.3137084989848 |

| 29 |
3 |
B_cells |
207 |
449 |
1.918803 |
2.297094 |
17068 |
1.2127959 |
0.00190089315938859 |
32.4444444444444 |
2.92709774940433 |
| 30 |
3 |
CD45 |
4863 |
11961 |
2.459593 |
2.661323 |
17068 |
28.4919147 |
0.368291539723459 |
6286 |
99.498743710662 |
| 31 |
3 |
CD8_T_cells |
4141 |
21377 |
3.926708 |
3.351746 |
17068 |
24.2617764 |
0.274255917506445 |
4681 |
85.1498678801089 |
| 32 |
3 |
Cytotoxic_cells |
5187 |
13357 |
2.174345 |
2.566798 |
17068 |
30.3902039 |
0.0463557534567612 |
791.2 |
15.6422504774729 |
| 33 |
3 |
DC |
8 |
8 |
1.000000 |
0.000000 |
17068 |
0.0468713 |
0.00015623779392235 |
2.66666666666667 |
0.942809041582063 |
| 34 |
3 |
Exhausted_CD8 |
1001 |
1495 |
1.477273 |
1.644003 |
17068 |
5.8647762 |
0.0161120224982423 |
275 |
9.08295106229247 |
| 35 |
3 |
Macrophages |
248 |
321 |
1.294355 |
1.309436 |
17068 |
1.4530115 |
0.0038229435200375 |
65.25 |
4.25 |
| 36 |
3 |
Mast_cells |
4 |
16 |
4.000000 |
3.464102 |
17068 |
0.0234357 |
8.78837590813218e-05 |
1.5 |
0.790569415042095 |
| 37 |
3 |
Neutrophils |
31 |
38 |
1.187500 |
1.060660 |
17068 |
0.1816264 |
0.000276206099969868 |
4.71428571428571 |
0.868966075756888 |
| 38 |
3 |
NK_CD56dim_cells |
137 |
173 |
1.262774 |
1.232346 |
17068 |
0.8026717 |
0.0020945629247715 |
35.75 |
3.11247489949718 |
| 39 |
3 |
NK_cells |
28 |
51 |
1.593750 |
1.881307 |
17068 |
0.1640497 |
0.000703070072650574 |
12 |
2.49443825784929 |
| 40 |
3 |
T_cells |
16150 |
139048 |
3.920711 |
3.382486 |
17068 |
94.6215139 |
0.601847511913132 |
10272.3333333333 |
93.5758753335733 |
| 41 |
3 |
Th1_cells |
64 |
82 |
1.281250 |
1.278252 |
17068 |
0.3749707 |
0.00392547457229904 |
67 |
8.54400374531753 |
| 42 |
3 |
Treg |
30 |
55 |
1.833333 |
2.166888 |
17068 |
0.1757675 |
0.00205062104523084 |
35 |
6.85565460040104 |

| 43 |
4 |
B_cells |
58 |
149 |
2.328125 |
2.678869 |
1768 |
3.2805430 |
0.0052790346907994 |
9.33333333333333 |
1.457208560956 |
| 44 |
4 |
CD45 |
265 |
585 |
2.207547 |
2.528313 |
1768 |
14.9886878 |
0.18947963800905 |
335 |
23 |
| 45 |
4 |
CD8_T_cells |
41 |
94 |
2.136364 |
2.445603 |
1768 |
2.3190045 |
0.0152714932126697 |
27 |
5 |
| 46 |
4 |
Cytotoxic_cells |
387 |
1881 |
3.329204 |
3.853424 |
1768 |
21.8891403 |
0.071606334841629 |
126.6 |
12.271919165314 |
| 47 |
4 |
DC |
1 |
1 |
1.000000 |
NA |
1768 |
0.0565611 |
0.000188536953242836 |
0.333333333333333 |
0.333333333333333 |
| 48 |
4 |
Exhausted_CD8 |
99 |
151 |
1.480392 |
1.657449 |
1768 |
5.5995475 |
0.0156957013574661 |
27.75 |
2.92617497767991 |
| 49 |
4 |
Macrophages |
391 |
769 |
1.835322 |
2.167417 |
1768 |
22.1153846 |
0.0698529411764706 |
123.5 |
6.97316284049068 |
| 50 |
4 |
Neutrophils |
546 |
1239 |
1.998387 |
2.303681 |
1768 |
30.8823529 |
0.0601163542340013 |
106.285714285714 |
5.15870573864794 |
| 51 |
4 |
NK_CD56dim_cells |
7 |
19 |
2.714286 |
2.927700 |
1768 |
0.3959276 |
0.00127262443438914 |
2.25 |
0.901387818865997 |
| 52 |
4 |
NK_cells |
9 |
11 |
1.000000 |
0.000000 |
1768 |
0.5090498 |
0.00207390648567119 |
3.66666666666667 |
1.29099444873581 |
| 53 |
4 |
T_cells |
259 |
719 |
2.152695 |
2.487936 |
1768 |
14.6493213 |
0.0394984917043741 |
69.8333333333333 |
5.39804491356722 |
| 54 |
4 |
Th1_cells |
8 |
8 |
1.000000 |
0.000000 |
1768 |
0.4524887 |
0.00452488687782805 |
8 |
2.82842712474619 |

| 55 |
5 |
CD45 |
2 |
2 |
1.000000 |
0.000000 |
75 |
2.666667 |
0.0266666666666667 |
2 |
1.4142135623731 |
| 56 |
5 |
CD8_T_cells |
1 |
7 |
7.000000 |
NA |
75 |
1.333333 |
0.0133333333333333 |
1 |
1 |
| 57 |
5 |
Cytotoxic_cells |
21 |
147 |
3.769231 |
4.836601 |
75 |
28.000000 |
0.192 |
14.4 |
6.81028633759257 |
| 58 |
5 |
Macrophages |
34 |
177 |
5.205882 |
3.207750 |
75 |
45.333333 |
0.223333333333333 |
16.75 |
3.17214438511238 |
| 59 |
5 |
NK_cells |
1 |
1 |
1.000000 |
NA |
75 |
1.333333 |
0.00444444444444444 |
0.333333333333333 |
0.333333333333333 |
| 60 |
5 |
T_cells |
6 |
35 |
3.181818 |
3.027150 |
75 |
8.000000 |
0.0333333333333333 |
2.5 |
1.21335164821342 |
| 61 |
5 |
Th1_cells |
1 |
1 |
1.000000 |
NA |
75 |
1.333333 |
0.0133333333333333 |
1 |
1 |

| 62 |
6 |
B_cells |
2187 |
21816 |
4.088456 |
3.623682 |
2282 |
95.8369851 |
0.507400915376375 |
1157.88888888889 |
29.179097879928 |
| 63 |
6 |
CD45 |
539 |
1249 |
2.317254 |
2.580579 |
2282 |
23.6196319 |
0.299737072743208 |
684 |
32.7414110874898 |
| 64 |
6 |
CD8_T_cells |
59 |
149 |
2.191177 |
2.638732 |
2282 |
2.5854514 |
0.0195004382120947 |
44.5 |
7.19374728496908 |
| 65 |
6 |
Cytotoxic_cells |
377 |
2065 |
3.542024 |
4.473811 |
2282 |
16.5205960 |
0.0629710780017528 |
143.7 |
18.3191156991816 |
| 66 |
6 |
Exhausted_CD8 |
59 |
77 |
1.305085 |
1.329431 |
2282 |
2.5854514 |
0.00679228746713409 |
15.5 |
2.06155281280883 |
| 67 |
6 |
Macrophages |
82 |
116 |
1.397590 |
1.592205 |
2282 |
3.5933392 |
0.00996932515337423 |
22.75 |
2.70416345659799 |
| 68 |
6 |
Mast_cells |
1 |
1 |
1.000000 |
NA |
2282 |
0.0438212 |
0.000109553023663453 |
0.25 |
0.25 |
| 69 |
6 |
Neutrophils |
20 |
20 |
1.000000 |
0.000000 |
2282 |
0.8764242 |
0.00125203455615375 |
2.85714285714286 |
0.63887656499994 |
| 70 |
6 |
NK_CD56dim_cells |
20 |
20 |
1.000000 |
0.000000 |
2282 |
0.8764242 |
0.00219106047326906 |
5 |
1.11803398874989 |
| 71 |
6 |
NK_cells |
5 |
5 |
1.000000 |
0.000000 |
2282 |
0.2191060 |
0.000730353491089687 |
1.66666666666667 |
0.74535599249993 |
| 72 |
6 |
T_cells |
306 |
1375 |
2.846791 |
3.010584 |
2282 |
13.4092901 |
0.0511247443762781 |
116.666666666667 |
8.71461097493425 |
| 73 |
6 |
Th1_cells |
16 |
16 |
1.000000 |
0.000000 |
2282 |
0.7011394 |
0.007011393514461 |
16 |
4 |
| 74 |
6 |
Treg |
1 |
1 |
1.000000 |
NA |
2282 |
0.0438212 |
0.000438212094653812 |
1 |
1 |

| 75 |
7 |
B_cells |
74 |
270 |
2.477064 |
3.065931 |
5900 |
1.2542373 |
0.00340866290018832 |
20.1111111111111 |
3.70018351229927 |
| 76 |
7 |
CD45 |
2104 |
6099 |
2.898764 |
2.947910 |
5900 |
35.6610169 |
0.503220338983051 |
2969 |
73.4506637138154 |
| 77 |
7 |
CD8_T_cells |
2505 |
10733 |
3.266281 |
3.112894 |
5900 |
42.4576271 |
0.420847457627119 |
2483 |
58.2923665671587 |
| 78 |
7 |
Cytotoxic_cells |
5882 |
283649 |
7.918954 |
5.924657 |
5900 |
99.6949153 |
3.56294915254237 |
21021.4 |
295.397088678951 |
| 79 |
7 |
DC |
1 |
1 |
1.000000 |
NA |
5900 |
0.0169492 |
5.64971751412429e-05 |
0.333333333333333 |
0.333333333333333 |
| 80 |
7 |
Exhausted_CD8 |
996 |
1769 |
1.662594 |
1.924216 |
5900 |
16.8813559 |
0.0508050847457627 |
299.75 |
10.3591746775503 |
| 81 |
7 |
Macrophages |
92 |
151 |
1.641304 |
2.019583 |
5900 |
1.5593220 |
0.00449152542372881 |
26.5 |
3.20156211871642 |
| 82 |
7 |
Neutrophils |
12 |
12 |
1.000000 |
0.000000 |
5900 |
0.2033898 |
0.000290556900726392 |
1.71428571428571 |
0.494871659305394 |
| 83 |
7 |
NK_CD56dim_cells |
414 |
713 |
1.646651 |
1.908156 |
5900 |
7.0169492 |
0.0206779661016949 |
122 |
6.46142399166004 |
| 84 |
7 |
NK_cells |
1052 |
2835 |
2.304878 |
2.589437 |
5900 |
17.8305085 |
0.0887005649717514 |
523.333333333333 |
19.2064803878506 |
| 85 |
7 |
T_cells |
3853 |
33071 |
4.141641 |
3.509735 |
5900 |
65.3050847 |
0.419858757062147 |
2477.16666666667 |
47.8768675295747 |
| 86 |
7 |
Th1_cells |
848 |
1558 |
1.837264 |
2.108493 |
5900 |
14.3728814 |
0.165762711864407 |
978 |
35.6089876295297 |
| 87 |
7 |
Treg |
7 |
7 |
1.000000 |
0.000000 |
5900 |
0.1186441 |
0.0011864406779661 |
7 |
2.64575131106459 |

| 88 |
8 |
B_cells |
132 |
635 |
3.489011 |
3.303671 |
202 |
65.3465347 |
0.162266226622662 |
32.7777777777778 |
3.56076007976935 |
| 89 |
8 |
CD45 |
16 |
29 |
1.812500 |
2.227667 |
202 |
7.9207921 |
0.0940594059405941 |
19 |
5.19615242270663 |
| 90 |
8 |
CD8_T_cells |
6 |
18 |
3.000000 |
3.098387 |
202 |
2.9702970 |
0.0198019801980198 |
4 |
1.73205080756888 |
| 91 |
8 |
Cytotoxic_cells |
183 |
1727 |
7.256303 |
4.297662 |
202 |
90.5940594 |
0.521287128712871 |
105.3 |
10.0583298812477 |
| 92 |
8 |
Exhausted_CD8 |
3 |
3 |
1.000000 |
0.000000 |
202 |
1.4851485 |
0.00371287128712871 |
0.75 |
0.433012701892219 |
| 93 |
8 |
Macrophages |
59 |
170 |
2.575758 |
2.700773 |
202 |
29.2079208 |
0.10519801980198 |
21.25 |
3.07205143186113 |
| 94 |
8 |
Neutrophils |
8 |
8 |
1.000000 |
0.000000 |
202 |
3.9603960 |
0.00565770862800566 |
1.14285714285714 |
0.404061017820884 |
| 95 |
8 |
NK_CD56dim_cells |
1 |
1 |
1.000000 |
NA |
202 |
0.4950495 |
0.00123762376237624 |
0.25 |
0.25 |
| 96 |
8 |
NK_cells |
1 |
1 |
1.000000 |
NA |
202 |
0.4950495 |
0.00165016501650165 |
0.333333333333333 |
0.333333333333333 |
| 97 |
8 |
T_cells |
35 |
176 |
3.591837 |
3.174891 |
202 |
17.3267327 |
0.0627062706270627 |
12.6666666666667 |
2.53859103528797 |
| 98 |
8 |
Th1_cells |
2 |
2 |
1.000000 |
0.000000 |
202 |
0.9900990 |
0.0099009900990099 |
2 |
1.4142135623731 |

| 99 |
9 |
B_cells |
1 |
1 |
1.0 |
NA |
25 |
4 |
0.00444444444444444 |
0.111111111111111 |
0.111111111111111 |
| 100 |
9 |
Cytotoxic_cells |
4 |
4 |
1.0 |
0.000000 |
25 |
16 |
0.016 |
0.4 |
0.2 |
| 101 |
9 |
Macrophages |
10 |
16 |
1.6 |
1.897367 |
25 |
40 |
0.11 |
2.75 |
0.901387818865997 |
| 102 |
9 |
T_cells |
2 |
2 |
1.0 |
0.000000 |
25 |
8 |
0.0133333333333333 |
0.333333333333333 |
0.235702260395516 |

| 10 |
Macrophages |
1 |
1 |
1 |
NA |
1 |
100 |
0.25 |
0.25 |
0.25 |
| 10 |
Mast_cells |
1 |
9 |
3 |
3.464102 |
1 |
100 |
1 |
1 |
1 |
[1] 2 3 4 5 6 7 8 9 10 11